7d

7d

7d

test shapes

CMakeLists.txt

@@ -19,6 +19,9 @@ add_executable(testh5 src/test_hdf5_ifc.f90)
 target_link_libraries(testh5 PRIVATE hdf5oo)
 target_compile_options(testh5 PRIVATE -Wno-compare-reals)
 add_test(NAME h5oo COMMAND testh5)
+set_tests_properties(h5oo PROPERTIES FIXTURES_SETUP h5files)
 
-add_executable(shaper src/GetShape.f90)
-target_link_libraries(shaper PRIVATE hdf5oo)
+add_executable(shapes_check src/GetShape.f90)
+target_link_libraries(shapes_check PRIVATE hdf5oo)
+add_test(NAME ShapeCheck COMMAND shapes_check p5.h5 group69/flux_node)
+set_tests_properties(ShapeCheck PROPERTIES FIXTURES_REQUIRED h5files)

README.md

@@ -7,13 +7,12 @@ Straightforward single-file/module access to HDF5.
 Uses Fortran 2008 `submodule` for clean, templatable structure.
 This thin object-oriented modern Fortran library abstracts away the messy parts of HDF5 so that you can read/write various types/ranks of data with a single command.
 
-Polymorphic API with read/write integer / real32/64:
+Polymorphic API with read/write for types integer, real32, real64 with rank:
 
-* scalar
-* 1-D .. 6-D
+* scalar (0-D)
+* 1-D .. 7-D
 
 as well as character (string) variables and attributes.
-If you'd like higher-rank arrays, let us know via GitHub Issue.
 
 Tested on systems including 
 

src/hdf5_interface.f90

@@ -27,27 +27,35 @@ module hdf5_interface
 
 !> add group or dataset integer/real 
 generic, public   :: add => &
-hdf_add_group, hdf_add_int, hdf_add_int_1d, hdf_add_int_2d, hdf_add_int_3d, &
-hdf_add_real32, hdf_add_real32_1d, hdf_add_real32_2d, hdf_add_real32_3d, hdf_add_real32_4d, hdf_add_real32_5d, hdf_add_real32_6d, &
-hdf_add_real64, hdf_add_real64_1d, hdf_add_real64_2d, hdf_add_real64_3d, hdf_add_real64_4d, hdf_add_real64_5d, hdf_add_real64_6d, &
+hdf_add_group, hdf_add_int, hdf_add_int_1d, hdf_add_int_2d, hdf_add_int_3d, hdf_add_int_5d, hdf_add_int_6d, hdf_add_int_7d,&
+hdf_add_real32, hdf_add_real32_1d, hdf_add_real32_2d, hdf_add_real32_3d, &
+  hdf_add_real32_4d, hdf_add_real32_5d, hdf_add_real32_6d, hdf_add_real32_7d, &
+hdf_add_real64, hdf_add_real64_1d, hdf_add_real64_2d, hdf_add_real64_3d, &
+  hdf_add_real64_4d, hdf_add_real64_5d, hdf_add_real64_6d, hdf_add_real64_7d, &
 hdf_add_string
 
 !> get dataset integer/real
 generic, public   :: get => &
-hdf_get_int, hdf_get_int_1d, hdf_get_int_2d, hdf_get_int_3d,&
-hdf_get_real32, hdf_get_real32_1d, hdf_get_real32_2d, hdf_get_real32_3d, hdf_get_real32_4d, hdf_get_real32_5d, hdf_get_real32_6d, &
-hdf_get_real64, hdf_get_real64_1d, hdf_get_real64_2d, hdf_get_real64_3d, hdf_get_real64_4d, hdf_get_real64_5d, hdf_get_real64_6d, &
+hdf_get_int, hdf_get_int_1d, hdf_get_int_2d, hdf_get_int_3d, hdf_get_int_4d,hdf_get_int_5d, hdf_get_int_6d, hdf_get_int_7d,&
+hdf_get_real32, hdf_get_real32_1d, hdf_get_real32_2d, hdf_get_real32_3d, &
+  hdf_get_real32_4d, hdf_get_real32_5d, hdf_get_real32_6d, hdf_get_real32_7d, &
+hdf_get_real64, hdf_get_real64_1d, hdf_get_real64_2d, hdf_get_real64_3d, &
+  hdf_get_real64_4d, hdf_get_real64_5d, hdf_get_real64_6d, hdf_get_real64_7d,  &
 hdf_get_string
 
 
 !> private methods
 procedure,private :: hdf_add_group, &
-hdf_add_int, hdf_add_int_1d, hdf_add_int_2d, hdf_add_int_3d, &
-hdf_get_int, hdf_get_int_1d, hdf_get_int_2d, hdf_get_int_3d, &
-hdf_add_real32, hdf_add_real32_1d, hdf_add_real32_2d, hdf_add_real32_3d, hdf_add_real32_4d, hdf_add_real32_5d,  hdf_add_real32_6d, &
-hdf_add_real64, hdf_add_real64_1d, hdf_add_real64_2d, hdf_add_real64_3d, hdf_add_real64_4d, hdf_add_real64_5d, hdf_add_real64_6d, &
-hdf_get_real32, hdf_get_real32_1d, hdf_get_real32_2d, hdf_get_real32_3d, hdf_get_real32_4d, hdf_get_real32_5d, hdf_get_real32_6d, &
-hdf_get_real64, hdf_get_real64_1d, hdf_get_real64_2d, hdf_get_real64_3d, hdf_get_real64_4d, hdf_get_real64_5d, hdf_get_real64_6d, &
+hdf_add_int, hdf_add_int_1d, hdf_add_int_2d, hdf_add_int_3d, hdf_add_int_4d, hdf_add_int_5d, hdf_add_int_6d, hdf_add_int_7d, &
+hdf_get_int, hdf_get_int_1d, hdf_get_int_2d, hdf_get_int_3d, hdf_get_int_4d, hdf_get_int_5d, hdf_get_int_6d, hdf_get_int_7d, &
+hdf_add_real32, hdf_add_real32_1d, hdf_add_real32_2d, hdf_add_real32_3d, &
+  hdf_add_real32_4d, hdf_add_real32_5d, hdf_add_real32_6d, hdf_add_real32_7d, &
+hdf_add_real64, hdf_add_real64_1d, hdf_add_real64_2d, hdf_add_real64_3d, &
+  hdf_add_real64_4d, hdf_add_real64_5d, hdf_add_real64_6d, hdf_add_real64_7d, &
+hdf_get_real32, hdf_get_real32_1d, hdf_get_real32_2d, hdf_get_real32_3d, &
+  hdf_get_real32_4d, hdf_get_real32_5d, hdf_get_real32_6d, hdf_get_real32_7d, &
+hdf_get_real64, hdf_get_real64_1d, hdf_get_real64_2d, hdf_get_real64_3d, &
+  hdf_get_real64_4d, hdf_get_real64_5d, hdf_get_real64_6d, hdf_get_real64_7d, &
 hdf_add_string, hdf_get_string
 
 end type hdf5_file
@@ -104,6 +112,34 @@ module subroutine hdf_add_int_3d(self,dname,value, chunk_size)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_int_3d
 
+module subroutine hdf_add_int_4d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+integer, intent(in) :: value(:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_int_4d
+
+module subroutine hdf_add_int_5d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+integer, intent(in) :: value(:,:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_int_5d
+
+module subroutine hdf_add_int_6d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+integer, intent(in) :: value(:,:,:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_int_6d
+
+module subroutine hdf_add_int_7d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+integer, intent(in) :: value(:,:,:,:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_int_7d
+
 module subroutine hdf_add_real64(self,dname,value)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
@@ -151,6 +187,13 @@ module subroutine hdf_add_real64_6d(self,dname,value, chunk_size)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_real64_6d
 
+module subroutine hdf_add_real64_7d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+real(real64), intent(in) :: value(:,:,:,:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_real64_7d
+
 module subroutine hdf_add_real32(self,dname,value)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
@@ -198,6 +241,13 @@ module subroutine hdf_add_real32_6d(self,dname,value, chunk_size)
 integer, intent(in), optional :: chunk_size(:)
 end subroutine hdf_add_real32_6d
 
+module subroutine hdf_add_real32_7d(self,dname,value, chunk_size)
+class(hdf5_file), intent(inout) :: self
+character(*), intent(in) :: dname
+real(real32), intent(in) :: value(:,:,:,:,:,:,:)
+integer, intent(in), optional :: chunk_size(:)
+end subroutine hdf_add_real32_7d
+
 module subroutine hdf_get_shape(self, dname, dims)
 class(hdf5_file), intent(in)     :: self
 character(*), intent(in)         :: dname
@@ -234,6 +284,31 @@ module subroutine hdf_get_int_3d(self, dname, value)
 integer, intent(out),allocatable :: value(:,:,:)
 end subroutine hdf_get_int_3d
 
+module subroutine hdf_get_int_4d(self, dname, value)
+class(hdf5_file), intent(in)     :: self
+character(*), intent(in)         :: dname
+integer, intent(out),allocatable :: value(:,:,:,:)
+end subroutine hdf_get_int_4d
+
+module subroutine hdf_get_int_5d(self, dname, value)
+class(hdf5_file), intent(in)     :: self
+character(*), intent(in)         :: dname
+integer, intent(out),allocatable :: value(:,:,:,:,:)
+end subroutine hdf_get_int_5d
+
+module subroutine hdf_get_int_6d(self, dname, value)
+class(hdf5_file), intent(in)     :: self
+character(*), intent(in)         :: dname
+integer, intent(out),allocatable :: value(:,:,:,:,:,:)
+end subroutine hdf_get_int_6d
+
+module subroutine hdf_get_int_7d(self, dname, value)
+class(hdf5_file), intent(in)     :: self
+character(*), intent(in)         :: dname
+integer, intent(out),allocatable :: value(:,:,:,:,:,:,:)
+end subroutine hdf_get_int_7d
+
+
 module subroutine hdf_get_real32(self, dname, value)
 class(hdf5_file), intent(in)  :: self
 character(*), intent(in)      :: dname
@@ -276,6 +351,12 @@ module subroutine hdf_get_real32_6d(self, dname, value)
 real(real32), intent(out),allocatable :: value(:,:,:,:,:,:)
 end subroutine hdf_get_real32_6d
 
+module subroutine hdf_get_real32_7d(self, dname, value)
+class(hdf5_file), intent(in)  :: self
+character(*), intent(in)      :: dname
+real(real32), intent(out),allocatable :: value(:,:,:,:,:,:,:)
+end subroutine hdf_get_real32_7d
+
 module subroutine hdf_get_real64(self, dname, value)
 class(hdf5_file), intent(in)  :: self
 character(*), intent(in)      :: dname
@@ -318,6 +399,12 @@ module subroutine hdf_get_real64_6d(self, dname, value)
 real(real64), intent(out),allocatable :: value(:,:,:,:,:,:)
 end subroutine hdf_get_real64_6d
 
+module subroutine hdf_get_real64_7d(self, dname, value)
+class(hdf5_file), intent(in)  :: self
+character(*), intent(in)      :: dname
+real(real64), intent(out),allocatable :: value(:,:,:,:,:,:,:)
+end subroutine hdf_get_real64_7d
+
 module subroutine hdf_open_group(self, gname)
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in)        :: gname

src/read_int.f90

@@ -13,8 +13,8 @@
 call h5dopen_f(self%lid, dname, dsid, ierr)
 if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
 
-! read dataset
-call h5dread_f(dsid, h5kind_to_type(kind(value),H5_INTEGER_KIND), value,int(shape(value),HSIZE_T), ierr)
+!> read dataset
+call h5dread_f(dsid, h5kind_to_type(kind(value),H5_REAL_KIND), value,int(shape(value),HSIZE_T), ierr)
 if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
 
 !> close dataset
@@ -75,4 +75,72 @@
 end procedure hdf_get_int_3d
 
 
+module procedure hdf_get_int_4d
+
+integer(HSIZE_T) :: dims(rank(value))
+integer(SIZE_T) :: dsize
+integer :: ierr, dtype
+
+call h5ltget_dataset_info_f(self%lid, dname, dims, dtype, dsize, ierr)
+if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
+
+allocate(value(dims(1),dims(2),dims(3),dims(4)))
+
+call h5ltread_dataset_f(self%lid, dname, h5kind_to_type(kind(value),H5_INTEGER_KIND), value, dims,  ierr)
+if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
+
+end procedure hdf_get_int_4d
+
+
+module procedure hdf_get_int_5d
+
+integer(HSIZE_T) :: dims(rank(value))
+integer(SIZE_T) :: dsize
+integer :: ierr, dtype
+
+call h5ltget_dataset_info_f(self%lid, dname, dims, dtype, dsize, ierr)
+if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
+
+allocate(value(dims(1),dims(2),dims(3),dims(4),dims(5)))
+
+call h5ltread_dataset_f(self%lid, dname, h5kind_to_type(kind(value),H5_INTEGER_KIND), value, dims,  ierr)
+if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
+
+end procedure hdf_get_int_5d
+
+
+module procedure hdf_get_int_6d
+
+integer(HSIZE_T) :: dims(rank(value))
+integer(SIZE_T) :: dsize
+integer :: ierr, dtype
+
+call h5ltget_dataset_info_f(self%lid, dname, dims, dtype, dsize, ierr)
+if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
+
+allocate(value(dims(1),dims(2),dims(3),dims(4),dims(5),dims(6)))
+
+call h5ltread_dataset_f(self%lid, dname, h5kind_to_type(kind(value),H5_INTEGER_KIND), value, dims,  ierr)
+if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
+
+end procedure hdf_get_int_6d
+
+
+module procedure hdf_get_int_7d
+
+integer(HSIZE_T) :: dims(rank(value))
+integer(SIZE_T) :: dsize
+integer :: ierr, dtype
+
+call h5ltget_dataset_info_f(self%lid, dname, dims, dtype, dsize, ierr)
+if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
+
+allocate(value(dims(1),dims(2),dims(3),dims(4),dims(5),dims(6),dims(7)))
+
+call h5ltread_dataset_f(self%lid, dname, h5kind_to_type(kind(value),H5_INTEGER_KIND), value, dims,  ierr)
+if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
+
+end procedure hdf_get_int_7d
+
+
 end submodule read_int

src/read_real32.f90

@@ -26,7 +26,7 @@
 
 module procedure hdf_get_real32_1d
 
-integer(HSIZE_T) :: dims(1)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -43,7 +43,7 @@
 
 module procedure hdf_get_real32_2d
 
-integer(HSIZE_T) :: dims(2)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -60,7 +60,7 @@
 
 module procedure hdf_get_real32_3d
 
-integer(HSIZE_T) :: dims(3)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -77,7 +77,7 @@
 
 module procedure hdf_get_real32_4d
 
-integer(HSIZE_T) :: dims(4)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -94,7 +94,7 @@
 
 module procedure hdf_get_real32_5d
 
-integer(HSIZE_T) :: dims(5)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -111,7 +111,7 @@
 
 module procedure hdf_get_real32_6d
 
-integer(HSIZE_T) :: dims(6)
+integer(HSIZE_T) :: dims(rank(value))
 integer(SIZE_T) :: dsize
 integer :: ierr, dtype
 
@@ -126,4 +126,21 @@
 end procedure hdf_get_real32_6d
 
 
+module procedure hdf_get_real32_7d
+
+integer(HSIZE_T) :: dims(rank(value))
+integer(SIZE_T) :: dsize
+integer :: ierr, dtype
+
+call h5ltget_dataset_info_f(self%lid, dname, dims, dtype, dsize, ierr)
+if (ierr /= 0) error stop 'error open dataset '//dname//' read '//self%filename
+
+allocate(value(dims(1),dims(2),dims(3),dims(4),dims(5),dims(6),dims(7)))
+
+call h5ltread_dataset_f(self%lid, dname, h5kind_to_type(kind(value),H5_REAL_KIND), value, dims,  ierr)
+if (ierr /= 0) error stop 'error read dataset '//dname//' read '//self%filename
+
+end procedure hdf_get_real32_7d
+
+
 end submodule read_real32